Contacts of the helix formed by residues 19 - 30 (chain Q) in PDB entry 5A0Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 19 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9Q THR* 6.4 0.9 - - - -
11Q ILE* 3.8 30.0 + - + +
13Q SER* 3.5 31.2 - - - -
14Q PRO* 4.2 11.7 - - + +
15Q GLU* 5.4 6.9 - - + +
18Q LEU* 1.4 69.5 - - - +
20Q GLN* 1.3 74.9 + - + +
22Q GLU* 3.2 16.4 + - - +
23Q TYR* 3.0 58.0 + + + -
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Residues in contact with GLN 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P THR* 3.2 29.3 - - - +
12P PHE* 3.3 35.7 + - - -
9Q THR* 4.0 29.3 - - - +
18Q LEU* 3.5 4.2 - - + +
19Q TYR* 1.3 84.6 - - + +
21Q VAL* 1.3 61.2 + - + +
23Q TYR* 3.8 18.3 - - - -
24Q ALA* 2.9 29.3 + - - +
122Q THR* 5.8 0.7 - - + -
128Q ARG* 4.3 7.1 - - - +
129Q PRO* 3.4 31.0 - - + +
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Residues in contact with VAL 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q LEU* 3.7 32.8 - - + +
19Q TYR 3.2 0.6 - - - -
20Q GLN* 1.3 77.7 - - + +
22Q GLU* 1.4 61.3 + - - +
24Q ALA* 3.3 6.5 + - - +
25Q MET* 3.1 33.8 + - + +
122Q THR* 3.9 28.5 - - + -
129Q PRO* 5.5 0.4 - - + -
152Q PRO 4.6 2.0 - - - +
153Q SER* 3.6 29.4 - - - +
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Residues in contact with GLU 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q GLU* 2.9 30.4 - - - +
17Q ARG* 3.1 28.9 + - + +
18Q LEU 3.0 18.1 + - - +
19Q TYR* 3.2 20.5 + - - +
21Q VAL* 1.4 77.5 - - + +
23Q TYR* 1.3 78.5 + - + +
25Q MET* 3.3 20.3 + - - +
26Q GLU* 3.3 19.0 + - + +
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Residues in contact with TYR 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.4 42.4 - - + -
13P SER 3.5 15.0 - - - +
14P PRO* 3.5 41.0 - - + +
16P GLY* 3.5 11.7 - - - +
19Q TYR* 3.0 45.2 + + + +
20Q GLN* 3.9 10.3 - - - +
22Q GLU* 1.3 92.5 - - + +
24Q ALA* 1.3 59.0 + - - +
26Q GLU* 3.3 7.3 + - - +
27Q ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 3.9 12.5 - - + -
20Q GLN 2.9 18.6 + - - +
21Q VAL* 3.5 6.5 - - - +
23Q TYR* 1.3 72.4 - - - +
25Q MET* 1.4 54.2 - - - +
26Q GLU 3.3 0.7 + - - -
27Q ALA* 3.4 6.3 + - - +
28Q ILE* 2.1 35.1 - - - +
129Q PRO* 5.3 2.9 - - + -
130Q PHE 4.7 1.3 - - - +
131Q GLY* 3.4 16.3 - - - +
152Q PRO* 3.6 30.3 - - + +
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Residues in contact with MET 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q VAL* 3.1 29.6 + - + +
22Q GLU* 3.3 13.7 + - - +
24Q ALA* 1.4 77.9 - - - +
26Q GLU* 1.4 61.1 + - + +
28Q ILE* 3.2 22.9 + - + +
29Q GLY 4.0 3.1 + - - -
133Q SER* 5.5 0.4 - - - +
151Q ASP* 3.1 26.5 - - - +
152Q PRO* 3.5 26.7 - - + -
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Residues in contact with GLU 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P PRO 3.0 21.3 - - - +
15P SER* 3.1 31.7 + - - +
22Q GLU* 3.3 17.5 - - - +
23Q TYR* 3.3 7.3 + - - +
24Q ALA 3.2 0.8 - - - -
25Q MET* 1.4 76.3 - - + +
27Q ALA* 1.3 63.4 + - - +
28Q ILE 3.2 2.0 - - - -
29Q GLY* 3.3 9.4 + - - +
30Q HIS* 3.2 13.0 + - - -
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Residues in contact with ALA 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 4.5 12.6 - - + -
15P SER 3.9 0.4 - - - -
16P GLY* 3.7 24.5 - - - +
23Q TYR 3.1 12.8 + - - +
24Q ALA* 3.4 13.2 + - - +
26Q GLU* 1.3 76.0 - - - +
28Q ILE* 1.3 61.8 - - - +
30Q HIS* 3.2 20.4 + - - +
31Q ALA 3.4 3.6 + - - -
78Q GLY 3.9 12.7 - - - +
79Q ILE* 5.0 8.2 - - + +
131Q GLY 4.4 8.1 - - - +
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Residues in contact with ILE 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q ALA 2.1 39.9 - - - +
25Q MET* 3.2 17.9 - - + +
27Q ALA* 1.3 73.7 - - - +
29Q GLY* 1.3 60.0 + - - +
30Q HIS 3.1 1.8 - - - -
31Q ALA* 2.7 38.8 + - + +
77Q ALA* 4.4 4.3 - - + -
78Q GLY* 4.1 7.2 - - - -
131Q GLY 3.3 18.4 - - - +
133Q SER* 3.6 14.6 - - - +
152Q PRO* 3.8 9.0 - - + -
164Q ILE* 3.7 31.6 - - + -
165Q GLY* 3.8 16.4 - - - +
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Residues in contact with GLY 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q MET 4.0 3.2 + - - -
26Q GLU* 3.3 11.1 + - - -
27Q ALA 3.3 1.0 - - - -
28Q ILE* 1.3 77.8 - - - +
30Q HIS* 1.4 59.1 + - - +
31Q ALA 3.4 3.3 - - - +
165Q GLY 4.8 3.1 - - - -
166Q ASN* 3.0 35.8 + - - +
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Residues in contact with HIS 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P SER* 3.4 34.7 + - - -
16P GLY 4.5 4.6 + - - +
17P LYS* 3.5 27.3 + - + -
26Q GLU 3.2 19.6 + - - -
27Q ALA* 3.2 11.1 + - - +
28Q ILE 3.1 0.4 - - - -
29Q GLY* 1.4 72.6 - - - +
31Q ALA* 1.4 64.0 + - - +
32Q GLY 3.8 0.7 + - - -
50Q ARG* 4.2 18.4 + - - -
166Q ASN* 4.9 4.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il